Paper- RNA-seq of tumor-educated platelets enables blood-based
Added on -2019-09-16
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Paper- RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass and molecular pathway cancer diagnostics”http://www.cell.com/action/showMethods?pii=S1535-6108%2815%2900349-9Data- https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68086I would like to do a comparison of methods for analyzing the RNA-Seq data in Myron G.Best et.al’s paper . The paper focused on Tumor-educated-blood platelets and their role in tumor growth They sequences 283 platelets from 6 difference tumor types. The primary tumor was correctly identified 71% of the time. There results show that blood platelets can give an indication of where the cancer will be found and can provide diagnostic advances in oncology. The data was analyzed by using voom. This will be under the limma package that we have used. I want to compare the analysis with edgeR and DESeq2. I believe seeing the similarities and differences in the type of analysis will show how important methodology is I reproducing an experiment. Method:Normalize and perform QC of the DataedgeR differential expression analysis voom differential expression analysis and comparison to results in the paper.DESeq2 differential expression analysis. The last part is the comparison of the three methodologies. I will show similarities , differences and which method worked the best in finding more differentially expressed genes.
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